The pronation of the first metatarsal (M1) in hallux valgus (HV) is currently the subject of a growing body of scientific research. However, several methods of manual measurement have been developed, providing heterogeneous results. Therefore, our objective was to develop semi-automatic 3D WBCT measurements to compare coronal rotation of M1 head relative to the ground, M1 intrinsic torsion and valgus deviation of M1 distal articular surface (DMAA) in HV and controls. Material and method : Forty-four symptomatic HV and 44 matched controls were retrospectively enrolled in this study, all of whom had undergone WBCT acquisition. Semi-automated bone segmentation was performed. Two methods have been developed to assess position of the M1 head. One was based on automatic fitting of a cylinder in the head, and the other on automatic selection of the position of the sesamoid gutters. Similarly, two methods have been developed to assess the position of the M1 base. One was defined using principal component analyses (PCA) of the proximal articular surface of M1, and the other using the longest diagonal of the M1 base. Results : The two groups did not differ according to age (p=0.71), sex (p=0.8) and BMI (p=1).First metatarsal head rotation relative to the ground was respectively 8.9±8.4 degrees and 2.1±6.4 degrees (cylinder method, p<0.001) and 9±8.3 degrees and 0.7±6.8 degrees (gutters method, p<0.001) in HV control groups. Combining the different sets of head and base measurements, the increase in M1 intrinsic torsion in pronation in HV ranged from 2 to 5 degrees. The DMAA was 11.4±6.9 degrees in the HV group and 5.6±4.7 degrees in the control group (p<0.001). Conclusion: Using semi-automatic 3D WBCT measurement we found that HV showed an increase in M1 head pronation relative to the ground of 7 to 8 degrees greater than controls, with an increase in M1 intrinsic torsion in pronation of 2 to 5 degrees and an increase in valgus deviation of the M1 distal articular surface of approximately 6 degrees